@Timothée Poisot, here are the specific details of what I need:
a script called 04_Validate_NCBI_Taxonomy.jl
It goes through every host and virus name in the file 'Virion/Virion-Master.csv'
It returns (as a host file and a virus file or fine to be merged) a file called "NCBIhierarchy.csv"
In that, it has the given and fuzzy-matched-plus-standardized valid names for every host and virus, plus taxonomy up to class level for both (note that host genus is currently missing entirely from VIRION, which is very funny)
I will then write an R script to take the flat file it writes out and edit virion-master based on it. (virion-master undergoes a few edits even after the flat file is created, and, that's okay. saves memory)
cjcarlson
commented
3 years ago
@Timothée Poisot, here are the specific details of what I need: a script called 04_Validate_NCBI_Taxonomy.jl It goes through every host and virus name in the file 'Virion/Virion-Master.csv' It returns (as a host file and a virus file or fine to be merged) a file called "NCBIhierarchy.csv" In that, it has the given and fuzzy-matched-plus-standardized valid names for every host and virus, plus taxonomy up to class level for both (note that host genus is currently missing entirely from VIRION, which is very funny) I will then write an R script to take the flat file it writes out and edit virion-master based on it. (virion-master undergoes a few edits even after the flat file is created, and, that's okay. saves memory)